I think GNOME3 is breaking *nix philosophy: do one thing and do it well; to be highly configurable. You have freedom to use compiz in GNOME2, but not in 3. There are a lot of good GTK2 themes but gitg and d-feet have hard-coded styles so only default GNOME3 theme will look sane. Super+p is somewhat hard-coded and you cannot customize it ... and there are more annoying issues. I am happy that mate-desktop is still alive.
No the difference is that GNOME is moving towards a 'product'. Everything is designed to work together, to be consistent everywhere. When you mix and match, you just get medicority because none of them were designed to work together at all. I would not call that even a Unix philosophy, it's just something that happened organically.
Doing what GNOME is doing is hard. Making hard choices on what to keep and what not. Fixing the things in the other parts of the stack instead of band aiding it in their own.
